Yes, whenever you sync with iTunes the first operation is to perform a backup of your device. However, the backup only includes your settings and app data. All your actual apps and music, photos (except camera roll), etc. are not included in the backup. They are synced separately during the process, so there would be no point storing them twice on your PC.
The backup process is incremental, meaning it only saves the delta changes each time you sync after the first full backup. This keeps it as efficient as possible.
If you ever need to restore from the backup you need to take a little care. Some users think the big "restore" button which is shown in iTunes is related to the backup. It is not!
To restore from backup, right-click on your iPad in the left column in iTunes when it is connected and then choose "restore from backup"
Hope that helps.